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When I read the documentation on http://www.prototypejs.org/api/ajax/periodicalUpdater I get the impression I should be able to call fileuploadStatus.stop() - for example in a link like this:
<a href="#" onclick="fileuploadStatus.stop();">stop</a> but it doesn't work, I get "stop is not a function" back from the browser debugger.

you'd need to call u.stop(), but 'u' will be local in scope to your function, if you need it to be global then lose the 'var' (and, I'd suggest, change the name to something a little more recognisable)